It took me only a second to figure it out, but once I did…wow thats awesome!!! User-ability wise, Id suggest making the add / subtract time buttons a bit more obvious or prominent, because at first I thought it was just a lil design thing around the words and was clicking away on the boxes…then clicking away at anything to see if I could find something to make it work.
Also, its not responsive… well, kind of in that it all does scale down for mobile, but in a way that it kinda just all squishes together. A super easy fix that would actually look great on mobile would be to have the session, timer and break blocks in columns that scale down to stack on top of each other for mobile view.
Hope that helps, but yeah, very awesome and unique…havnt seen a pomodoro like this before!